CDD: a Conserved Domain Database for protein classification

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. doi: 10.1093/nar/gki069.


The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed, and can be accessed at CD-Search, which is available at, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein-protein queries submitted to NCBI's BLAST search service at are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Conserved Sequence
  • Databases, Protein*
  • Phylogeny
  • Protein Structure, Tertiary*
  • Proteins / classification*
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface


  • Proteins